Multiple sequence alignment - TraesCS5D01G469000

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5D01G469000 chr5D 100.000 2960 0 0 1 2960 510129561 510126602 0.000000e+00 5467.0
1 TraesCS5D01G469000 chr5D 93.855 830 48 3 636 1465 510163950 510163124 0.000000e+00 1247.0
2 TraesCS5D01G469000 chr5D 92.091 569 44 1 1628 2195 510163121 510162553 0.000000e+00 800.0
3 TraesCS5D01G469000 chr5D 85.127 632 62 19 25 647 510164587 510163979 4.190000e-173 617.0
4 TraesCS5D01G469000 chr5D 91.429 280 19 3 2622 2898 510161755 510161478 2.150000e-101 379.0
5 TraesCS5D01G469000 chr5D 86.799 303 26 7 2295 2596 510162363 510162074 2.850000e-85 326.0
6 TraesCS5D01G469000 chr5D 100.000 43 0 0 2196 2238 510162526 510162484 2.450000e-11 80.5
7 TraesCS5D01G469000 chr5B 91.245 2353 127 41 2 2291 641134980 641132644 0.000000e+00 3131.0
8 TraesCS5D01G469000 chr5B 83.607 183 24 6 1449 1627 125795057 125794877 1.820000e-37 167.0
9 TraesCS5D01G469000 chr5A 90.483 704 50 8 425 1122 638604757 638604065 0.000000e+00 913.0
10 TraesCS5D01G469000 chr5A 90.033 612 36 9 1629 2238 638603583 638602995 0.000000e+00 769.0
11 TraesCS5D01G469000 chr5A 92.966 526 27 7 6 521 638605283 638604758 0.000000e+00 758.0
12 TraesCS5D01G469000 chr5A 93.605 344 18 2 1121 1464 638603927 638603588 7.320000e-141 510.0
13 TraesCS5D01G469000 chr5A 84.153 183 23 6 1449 1627 368099323 368099503 3.920000e-39 172.0
14 TraesCS5D01G469000 chr3A 81.724 290 49 4 1788 2076 65893104 65893390 3.810000e-59 239.0
15 TraesCS5D01G469000 chr3A 87.288 118 15 0 966 1083 65736872 65736755 5.150000e-28 135.0
16 TraesCS5D01G469000 chr1A 84.699 183 22 6 1449 1627 401681592 401681772 8.430000e-41 178.0
17 TraesCS5D01G469000 chr1A 84.239 184 21 8 1449 1627 96444264 96444084 3.920000e-39 172.0
18 TraesCS5D01G469000 chr3B 84.153 183 23 6 1449 1627 426997827 426998007 3.920000e-39 172.0
19 TraesCS5D01G469000 chr3B 87.000 100 13 0 984 1083 86130393 86130294 2.410000e-21 113.0
20 TraesCS5D01G469000 chr4A 83.607 183 24 6 1449 1627 63749957 63750137 1.820000e-37 167.0
21 TraesCS5D01G469000 chr4A 83.060 183 25 6 1449 1627 492347019 492346839 8.490000e-36 161.0
22 TraesCS5D01G469000 chr2B 83.152 184 23 8 1449 1627 214001980 214001800 8.490000e-36 161.0
23 TraesCS5D01G469000 chr3D 89.831 118 12 0 966 1083 55532487 55532604 5.110000e-33 152.0
24 TraesCS5D01G469000 chr3D 94.000 100 6 0 984 1083 55918512 55918611 5.110000e-33 152.0
25 TraesCS5D01G469000 chr3D 89.344 122 12 1 1773 1893 56570760 56570881 5.110000e-33 152.0
26 TraesCS5D01G469000 chr3D 94.231 52 3 0 1032 1083 55768729 55768780 2.450000e-11 80.5
27 TraesCS5D01G469000 chr3D 94.231 52 3 0 1032 1083 55776835 55776886 2.450000e-11 80.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G469000 chr5D 510126602 510129561 2959 True 5467.000000 5467 100.000000 1 2960 1 chr5D.!!$R1 2959
1 TraesCS5D01G469000 chr5D 510161478 510164587 3109 True 574.916667 1247 91.550167 25 2898 6 chr5D.!!$R2 2873
2 TraesCS5D01G469000 chr5B 641132644 641134980 2336 True 3131.000000 3131 91.245000 2 2291 1 chr5B.!!$R2 2289
3 TraesCS5D01G469000 chr5A 638602995 638605283 2288 True 737.500000 913 91.771750 6 2238 4 chr5A.!!$R1 2232

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
262 272 0.178301 TGCCCGCATTAATCCGTGTA 59.822 50.0 0.0 0.0 0.0 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2016 2342 1.024271 CACTGCCCATTATGAACCCG 58.976 55.0 0.0 0.0 0.0 5.28 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 2.860293 CGCGCTCGTTCCATTTGT 59.140 55.556 5.56 0.00 0.00 2.83
40 43 1.953559 TGTGCTTGTTCAGACCTCAC 58.046 50.000 0.00 0.00 0.00 3.51
262 272 0.178301 TGCCCGCATTAATCCGTGTA 59.822 50.000 0.00 0.00 0.00 2.90
272 282 5.049680 GCATTAATCCGTGTAACCATCGATT 60.050 40.000 0.00 0.00 0.00 3.34
306 316 0.814457 AGTTTCAACTGCAACGCCAA 59.186 45.000 0.00 0.00 37.98 4.52
321 331 0.179105 GCCAATGCGCCAATCAATCA 60.179 50.000 4.18 0.00 0.00 2.57
325 340 0.818938 ATGCGCCAATCAATCAAGCA 59.181 45.000 4.18 0.00 37.54 3.91
343 359 6.480763 TCAAGCACAAATTAAGGATCTACCA 58.519 36.000 0.00 0.00 42.04 3.25
476 507 0.393132 GCAAGAGTACTCCCAAGGGC 60.393 60.000 19.38 10.15 34.68 5.19
547 675 8.038944 TGTTCTACAGTAATTCCTATGGTTGTC 58.961 37.037 0.00 0.00 0.00 3.18
553 681 3.832615 ATTCCTATGGTTGTCCCGTAC 57.167 47.619 0.00 0.00 35.15 3.67
555 683 0.466963 CCTATGGTTGTCCCGTACCC 59.533 60.000 0.00 0.00 35.15 3.69
556 684 1.492764 CTATGGTTGTCCCGTACCCT 58.507 55.000 0.00 0.00 35.15 4.34
557 685 1.138266 CTATGGTTGTCCCGTACCCTG 59.862 57.143 0.00 0.00 35.15 4.45
621 755 3.836365 TCTTGTGTTGGTCATCACTCA 57.164 42.857 11.81 1.23 35.82 3.41
623 757 4.067192 TCTTGTGTTGGTCATCACTCATG 58.933 43.478 11.81 0.00 35.82 3.07
624 758 2.781923 TGTGTTGGTCATCACTCATGG 58.218 47.619 11.81 0.00 35.82 3.66
695 870 7.607607 TGGCTAGCAATCGTTGATAATCATAAT 59.392 33.333 18.24 0.00 30.24 1.28
714 889 0.250295 TGTGTGTGAACTAGCTGGGC 60.250 55.000 0.85 0.00 0.00 5.36
798 974 7.609760 ACTGCAATCGTATTTTTCAGACATA 57.390 32.000 0.00 0.00 0.00 2.29
816 992 5.578336 AGACATATATGTATCACATGCACGC 59.422 40.000 18.28 1.74 41.95 5.34
832 1008 4.249661 TGCACGCAATTAGACATTCTACA 58.750 39.130 0.00 0.00 0.00 2.74
833 1009 4.875536 TGCACGCAATTAGACATTCTACAT 59.124 37.500 0.00 0.00 0.00 2.29
834 1010 5.353956 TGCACGCAATTAGACATTCTACATT 59.646 36.000 0.00 0.00 0.00 2.71
907 1085 5.689383 TCACAAATTTTAGCCAGAGTGAC 57.311 39.130 0.00 0.00 30.64 3.67
915 1093 1.342074 AGCCAGAGTGACTAGTTGCA 58.658 50.000 0.00 0.00 0.00 4.08
925 1103 5.821204 AGTGACTAGTTGCATTTGTTTCAC 58.179 37.500 0.00 0.00 0.00 3.18
947 1125 5.069648 CACATGTCTTAGATCTAGCCTTGGA 59.930 44.000 2.02 0.00 0.00 3.53
948 1126 5.663106 ACATGTCTTAGATCTAGCCTTGGAA 59.337 40.000 2.02 0.00 0.00 3.53
949 1127 6.328672 ACATGTCTTAGATCTAGCCTTGGAAT 59.671 38.462 2.02 0.00 0.00 3.01
950 1128 6.814954 TGTCTTAGATCTAGCCTTGGAATT 57.185 37.500 2.02 0.00 0.00 2.17
1096 1278 4.599041 TGTAATATTGCACCTTTGGCTCT 58.401 39.130 1.68 0.00 0.00 4.09
1251 1572 1.254026 CCGATATCGCCCTGGAACTA 58.746 55.000 19.78 0.00 38.18 2.24
1310 1631 7.613247 CATTGCTTGGATTATTATGACGTTG 57.387 36.000 0.00 0.00 0.00 4.10
1331 1652 3.814842 TGCTGTGTTTCATACTCTTGTGG 59.185 43.478 0.00 0.00 0.00 4.17
1340 1661 6.978674 TTCATACTCTTGTGGTCCTATAGG 57.021 41.667 13.07 13.07 0.00 2.57
1385 1706 5.396436 GGGCACAGAGCTACTTATAAGGAAA 60.396 44.000 16.73 1.43 44.79 3.13
1386 1707 6.292150 GGCACAGAGCTACTTATAAGGAAAT 58.708 40.000 16.73 0.00 44.79 2.17
1391 1712 9.214962 ACAGAGCTACTTATAAGGAAATTACCT 57.785 33.333 16.73 1.86 42.69 3.08
1441 1762 4.306600 CAGTTTTGCAAGGTACATTTCCC 58.693 43.478 0.00 0.00 0.00 3.97
1661 1982 3.188460 ACGAACAAATCCAACTCAATCCG 59.812 43.478 0.00 0.00 0.00 4.18
1662 1983 3.435327 CGAACAAATCCAACTCAATCCGA 59.565 43.478 0.00 0.00 0.00 4.55
1941 2265 4.046286 TGTGTATTTGGCAAGGAGGATT 57.954 40.909 0.00 0.00 0.00 3.01
1995 2321 2.291475 TGGATCAAGCCCAGCATGTTTA 60.291 45.455 0.00 0.00 0.00 2.01
1996 2322 2.360165 GGATCAAGCCCAGCATGTTTAG 59.640 50.000 0.00 0.00 0.00 1.85
2016 2342 4.525912 AGTGCTTTCCATGTGATTTTCC 57.474 40.909 0.00 0.00 0.00 3.13
2244 2613 2.280254 CGTTGTACGTGGGGCACA 60.280 61.111 0.00 0.00 36.74 4.57
2291 2661 3.791973 TTTTAAATGCCTGGGTATGCG 57.208 42.857 0.00 0.00 0.00 4.73
2452 2868 8.740123 TTTTCCTTTTACTTTTTCATTTCCCC 57.260 30.769 0.00 0.00 0.00 4.81
2453 2869 7.439108 TTCCTTTTACTTTTTCATTTCCCCA 57.561 32.000 0.00 0.00 0.00 4.96
2454 2870 7.625498 TCCTTTTACTTTTTCATTTCCCCAT 57.375 32.000 0.00 0.00 0.00 4.00
2455 2871 8.040002 TCCTTTTACTTTTTCATTTCCCCATT 57.960 30.769 0.00 0.00 0.00 3.16
2456 2872 8.498575 TCCTTTTACTTTTTCATTTCCCCATTT 58.501 29.630 0.00 0.00 0.00 2.32
2465 2881 5.083533 TCATTTCCCCATTTTCCAATTCG 57.916 39.130 0.00 0.00 0.00 3.34
2466 2882 4.530161 TCATTTCCCCATTTTCCAATTCGT 59.470 37.500 0.00 0.00 0.00 3.85
2467 2883 4.965200 TTTCCCCATTTTCCAATTCGTT 57.035 36.364 0.00 0.00 0.00 3.85
2524 2940 6.942224 GTGCGAACACATGAATTTTAAATTCG 59.058 34.615 20.91 12.65 46.61 3.34
2609 3328 7.907214 ACAATGTCTTATCTAAGTTGTGGTC 57.093 36.000 4.54 0.00 32.37 4.02
2610 3329 7.680730 ACAATGTCTTATCTAAGTTGTGGTCT 58.319 34.615 4.54 0.00 32.37 3.85
2611 3330 8.812972 ACAATGTCTTATCTAAGTTGTGGTCTA 58.187 33.333 4.54 0.00 32.37 2.59
2612 3331 9.823647 CAATGTCTTATCTAAGTTGTGGTCTAT 57.176 33.333 0.00 0.00 34.93 1.98
2614 3333 8.008513 TGTCTTATCTAAGTTGTGGTCTATCC 57.991 38.462 0.00 0.00 34.93 2.59
2615 3334 7.140048 GTCTTATCTAAGTTGTGGTCTATCCG 58.860 42.308 0.00 0.00 35.43 4.18
2616 3335 7.013083 GTCTTATCTAAGTTGTGGTCTATCCGA 59.987 40.741 0.00 0.00 35.43 4.55
2617 3336 7.724506 TCTTATCTAAGTTGTGGTCTATCCGAT 59.275 37.037 0.00 0.00 35.43 4.18
2618 3337 5.769484 TCTAAGTTGTGGTCTATCCGATC 57.231 43.478 0.00 0.00 39.52 3.69
2619 3338 5.446860 TCTAAGTTGTGGTCTATCCGATCT 58.553 41.667 0.00 0.00 39.52 2.75
2620 3339 6.598503 TCTAAGTTGTGGTCTATCCGATCTA 58.401 40.000 0.00 0.00 39.52 1.98
2621 3340 7.058525 TCTAAGTTGTGGTCTATCCGATCTAA 58.941 38.462 0.00 0.00 39.52 2.10
2622 3341 5.517322 AGTTGTGGTCTATCCGATCTAAC 57.483 43.478 0.00 0.00 39.52 2.34
2623 3342 5.202004 AGTTGTGGTCTATCCGATCTAACT 58.798 41.667 0.00 0.00 39.52 2.24
2624 3343 5.067936 AGTTGTGGTCTATCCGATCTAACTG 59.932 44.000 0.00 0.00 39.52 3.16
2625 3344 4.533815 TGTGGTCTATCCGATCTAACTGT 58.466 43.478 0.00 0.00 39.52 3.55
2637 3356 5.800941 CCGATCTAACTGTTATAATCTCCGC 59.199 44.000 15.36 0.00 0.00 5.54
2651 3370 1.284785 TCTCCGCCCAAATTTGATCCT 59.715 47.619 19.86 0.00 0.00 3.24
2666 3385 2.294233 TGATCCTGCTTTGTTCTTGTGC 59.706 45.455 0.00 0.00 0.00 4.57
2667 3386 0.662619 TCCTGCTTTGTTCTTGTGCG 59.337 50.000 0.00 0.00 0.00 5.34
2707 3426 1.683790 CCTCCGTTGTCGCGATGTTC 61.684 60.000 14.06 0.00 35.54 3.18
2725 3444 6.565060 CGATGTTCATTTGTCGGACTGTTTTA 60.565 38.462 9.88 0.00 0.00 1.52
2733 3452 2.998670 GTCGGACTGTTTTAGTTAGGCC 59.001 50.000 0.00 0.00 40.53 5.19
2735 3454 3.056322 TCGGACTGTTTTAGTTAGGCCTC 60.056 47.826 9.68 0.00 40.53 4.70
2805 3526 4.556233 TGTGTCCAGAAACAGAATAGACG 58.444 43.478 0.00 0.00 0.00 4.18
2806 3527 4.038763 TGTGTCCAGAAACAGAATAGACGT 59.961 41.667 0.00 0.00 0.00 4.34
2811 3532 4.556233 CAGAAACAGAATAGACGTGGTGA 58.444 43.478 0.00 0.00 0.00 4.02
2849 3571 2.718062 TCCCATCACCTCCATTATGCAT 59.282 45.455 3.79 3.79 0.00 3.96
2894 3616 3.181429 TGCTCTCTTCATTTCCCCTTTGT 60.181 43.478 0.00 0.00 0.00 2.83
2898 3620 5.705400 TCTCTTCATTTCCCCTTTGTCTTT 58.295 37.500 0.00 0.00 0.00 2.52
2899 3621 5.770162 TCTCTTCATTTCCCCTTTGTCTTTC 59.230 40.000 0.00 0.00 0.00 2.62
2900 3622 5.454062 TCTTCATTTCCCCTTTGTCTTTCA 58.546 37.500 0.00 0.00 0.00 2.69
2901 3623 6.077322 TCTTCATTTCCCCTTTGTCTTTCAT 58.923 36.000 0.00 0.00 0.00 2.57
2902 3624 6.554605 TCTTCATTTCCCCTTTGTCTTTCATT 59.445 34.615 0.00 0.00 0.00 2.57
2903 3625 7.728083 TCTTCATTTCCCCTTTGTCTTTCATTA 59.272 33.333 0.00 0.00 0.00 1.90
2904 3626 7.466746 TCATTTCCCCTTTGTCTTTCATTAG 57.533 36.000 0.00 0.00 0.00 1.73
2905 3627 7.237982 TCATTTCCCCTTTGTCTTTCATTAGA 58.762 34.615 0.00 0.00 0.00 2.10
2906 3628 7.394359 TCATTTCCCCTTTGTCTTTCATTAGAG 59.606 37.037 0.00 0.00 0.00 2.43
2907 3629 4.589908 TCCCCTTTGTCTTTCATTAGAGC 58.410 43.478 0.00 0.00 0.00 4.09
2908 3630 3.696548 CCCCTTTGTCTTTCATTAGAGCC 59.303 47.826 0.00 0.00 0.00 4.70
2909 3631 3.375299 CCCTTTGTCTTTCATTAGAGCCG 59.625 47.826 0.00 0.00 0.00 5.52
2910 3632 4.253685 CCTTTGTCTTTCATTAGAGCCGA 58.746 43.478 0.00 0.00 0.00 5.54
2911 3633 4.093556 CCTTTGTCTTTCATTAGAGCCGAC 59.906 45.833 0.00 0.00 0.00 4.79
2912 3634 4.537135 TTGTCTTTCATTAGAGCCGACT 57.463 40.909 0.00 0.00 0.00 4.18
2913 3635 5.654603 TTGTCTTTCATTAGAGCCGACTA 57.345 39.130 0.00 0.00 0.00 2.59
2914 3636 5.854010 TGTCTTTCATTAGAGCCGACTAT 57.146 39.130 0.00 0.00 0.00 2.12
2915 3637 6.222038 TGTCTTTCATTAGAGCCGACTATT 57.778 37.500 0.00 0.00 0.00 1.73
2916 3638 6.640518 TGTCTTTCATTAGAGCCGACTATTT 58.359 36.000 0.00 0.00 0.00 1.40
2917 3639 7.103641 TGTCTTTCATTAGAGCCGACTATTTT 58.896 34.615 0.00 0.00 0.00 1.82
2918 3640 7.606456 TGTCTTTCATTAGAGCCGACTATTTTT 59.394 33.333 0.00 0.00 0.00 1.94
2919 3641 7.905493 GTCTTTCATTAGAGCCGACTATTTTTG 59.095 37.037 0.00 0.00 0.00 2.44
2920 3642 7.606456 TCTTTCATTAGAGCCGACTATTTTTGT 59.394 33.333 0.00 0.00 0.00 2.83
2921 3643 6.662414 TCATTAGAGCCGACTATTTTTGTG 57.338 37.500 0.00 0.00 0.00 3.33
2922 3644 6.170506 TCATTAGAGCCGACTATTTTTGTGT 58.829 36.000 0.00 0.00 0.00 3.72
2923 3645 5.856126 TTAGAGCCGACTATTTTTGTGTG 57.144 39.130 0.00 0.00 0.00 3.82
2924 3646 3.074412 AGAGCCGACTATTTTTGTGTGG 58.926 45.455 0.00 0.00 0.00 4.17
2925 3647 1.539827 AGCCGACTATTTTTGTGTGGC 59.460 47.619 0.00 0.00 41.50 5.01
2926 3648 1.268352 GCCGACTATTTTTGTGTGGCA 59.732 47.619 0.00 0.00 40.88 4.92
2927 3649 2.094752 GCCGACTATTTTTGTGTGGCAT 60.095 45.455 0.00 0.00 40.88 4.40
2928 3650 3.613910 GCCGACTATTTTTGTGTGGCATT 60.614 43.478 0.00 0.00 40.88 3.56
2929 3651 4.555262 CCGACTATTTTTGTGTGGCATTT 58.445 39.130 0.00 0.00 0.00 2.32
2930 3652 4.987912 CCGACTATTTTTGTGTGGCATTTT 59.012 37.500 0.00 0.00 0.00 1.82
2931 3653 5.465056 CCGACTATTTTTGTGTGGCATTTTT 59.535 36.000 0.00 0.00 0.00 1.94
2952 3674 3.782656 TTCCTAGTTTCAACTCCACCC 57.217 47.619 0.00 0.00 40.37 4.61
2953 3675 2.986050 TCCTAGTTTCAACTCCACCCT 58.014 47.619 0.00 0.00 40.37 4.34
2954 3676 2.904434 TCCTAGTTTCAACTCCACCCTC 59.096 50.000 0.00 0.00 40.37 4.30
2955 3677 2.353803 CCTAGTTTCAACTCCACCCTCG 60.354 54.545 0.00 0.00 40.37 4.63
2956 3678 1.420430 AGTTTCAACTCCACCCTCGA 58.580 50.000 0.00 0.00 32.86 4.04
2957 3679 1.766496 AGTTTCAACTCCACCCTCGAA 59.234 47.619 0.00 0.00 32.86 3.71
2958 3680 2.372172 AGTTTCAACTCCACCCTCGAAT 59.628 45.455 0.00 0.00 32.86 3.34
2959 3681 3.146847 GTTTCAACTCCACCCTCGAATT 58.853 45.455 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 0.880278 GCGTGAGGTCTGAACAAGCA 60.880 55.000 0.00 0.00 38.46 3.91
73 76 0.512518 TCGTCATGTTTGCTGCTTCG 59.487 50.000 0.00 0.00 0.00 3.79
78 81 1.664016 GCAACCTCGTCATGTTTGCTG 60.664 52.381 0.00 0.00 0.00 4.41
89 96 1.867919 CTCTCAGTCGGCAACCTCGT 61.868 60.000 0.00 0.00 0.00 4.18
262 272 0.742505 TACGGCTCGAATCGATGGTT 59.257 50.000 5.59 0.00 34.61 3.67
272 282 0.806868 AAACTGATCGTACGGCTCGA 59.193 50.000 16.52 0.00 41.45 4.04
306 316 0.818938 TGCTTGATTGATTGGCGCAT 59.181 45.000 10.83 0.00 0.00 4.73
321 331 7.451566 ACTTTGGTAGATCCTTAATTTGTGCTT 59.548 33.333 0.00 0.00 37.07 3.91
325 340 6.598064 CCGACTTTGGTAGATCCTTAATTTGT 59.402 38.462 0.00 0.00 37.07 2.83
343 359 0.940991 GGCACGTACGAACCGACTTT 60.941 55.000 24.41 0.00 0.00 2.66
489 520 2.871182 TACCTCTCGCAGTTGCTATG 57.129 50.000 2.29 0.00 39.32 2.23
547 675 3.387050 AGAAATACTAAGCAGGGTACGGG 59.613 47.826 0.00 0.00 0.00 5.28
553 681 5.128919 AGCATCAAGAAATACTAAGCAGGG 58.871 41.667 0.00 0.00 0.00 4.45
555 683 6.510799 CGGAAGCATCAAGAAATACTAAGCAG 60.511 42.308 0.00 0.00 0.00 4.24
556 684 5.294306 CGGAAGCATCAAGAAATACTAAGCA 59.706 40.000 0.00 0.00 0.00 3.91
557 685 5.277538 CCGGAAGCATCAAGAAATACTAAGC 60.278 44.000 0.00 0.00 0.00 3.09
695 870 0.250295 GCCCAGCTAGTTCACACACA 60.250 55.000 0.00 0.00 0.00 3.72
714 889 3.559069 AGGCCCAAGTGATCACATAATG 58.441 45.455 27.02 18.21 0.00 1.90
798 974 5.694231 AATTGCGTGCATGTGATACATAT 57.306 34.783 7.93 0.00 36.53 1.78
855 1033 4.090642 CGTGCTCTCGAAAGCCATATATTC 59.909 45.833 8.55 0.00 41.77 1.75
925 1103 5.798125 TCCAAGGCTAGATCTAAGACATG 57.202 43.478 3.57 4.03 0.00 3.21
1096 1278 1.070134 AGTTGCTAAGGTGCTTCGTCA 59.930 47.619 0.00 0.00 0.00 4.35
1251 1572 3.118775 TGCTACACATACCGAAGAGCAAT 60.119 43.478 0.00 0.00 35.63 3.56
1306 1627 4.024893 ACAAGAGTATGAAACACAGCAACG 60.025 41.667 0.00 0.00 0.00 4.10
1309 1630 3.814842 CCACAAGAGTATGAAACACAGCA 59.185 43.478 0.00 0.00 0.00 4.41
1310 1631 3.815401 ACCACAAGAGTATGAAACACAGC 59.185 43.478 0.00 0.00 0.00 4.40
1340 1661 5.523369 CCCTTCTGATATTTGCGAATTTCC 58.477 41.667 4.06 0.00 0.00 3.13
1385 1706 5.280215 CCTGACAAGTCTCTGGAAAGGTAAT 60.280 44.000 1.53 0.00 0.00 1.89
1386 1707 4.040461 CCTGACAAGTCTCTGGAAAGGTAA 59.960 45.833 1.53 0.00 0.00 2.85
1391 1712 2.634940 CTCCCTGACAAGTCTCTGGAAA 59.365 50.000 1.53 0.00 0.00 3.13
1421 1742 4.280929 AGAGGGAAATGTACCTTGCAAAAC 59.719 41.667 0.00 0.00 37.18 2.43
1518 1839 9.751542 CTCTAAAATAGGCTTATATACATCCGG 57.248 37.037 0.00 0.00 0.00 5.14
1616 1937 7.069578 TCGTATCTGAAATAAGCCTACTCCTTT 59.930 37.037 0.00 0.00 0.00 3.11
1618 1939 6.069331 TCGTATCTGAAATAAGCCTACTCCT 58.931 40.000 0.00 0.00 0.00 3.69
1677 1998 9.967451 TCTCTATACACCCTAATCAATCTCTAG 57.033 37.037 0.00 0.00 0.00 2.43
1932 2256 3.432051 CTCGCCGCGAATCCTCCTT 62.432 63.158 17.53 0.00 34.74 3.36
1995 2321 3.057315 CGGAAAATCACATGGAAAGCACT 60.057 43.478 0.00 0.00 0.00 4.40
1996 2322 3.244976 CGGAAAATCACATGGAAAGCAC 58.755 45.455 0.00 0.00 0.00 4.40
2016 2342 1.024271 CACTGCCCATTATGAACCCG 58.976 55.000 0.00 0.00 0.00 5.28
2175 2501 1.880027 GGTGACAGCCGATCAAAAACT 59.120 47.619 0.00 0.00 0.00 2.66
2188 2514 2.343101 TCGCGAAAAATAGGGTGACAG 58.657 47.619 6.20 0.00 0.00 3.51
2244 2613 7.398024 AGAACTCACAGCCTCTATAAAAACAT 58.602 34.615 0.00 0.00 0.00 2.71
2291 2661 7.784633 AGCTTAGCTCTTTGAATTCTACATC 57.215 36.000 0.00 0.00 30.62 3.06
2437 2853 6.259346 TGGAAAATGGGGAAATGAAAAAGT 57.741 33.333 0.00 0.00 0.00 2.66
2443 2859 4.530161 ACGAATTGGAAAATGGGGAAATGA 59.470 37.500 0.00 0.00 0.00 2.57
2445 2861 5.497464 AACGAATTGGAAAATGGGGAAAT 57.503 34.783 0.00 0.00 0.00 2.17
2446 2862 4.965200 AACGAATTGGAAAATGGGGAAA 57.035 36.364 0.00 0.00 0.00 3.13
2447 2863 7.906199 ATATAACGAATTGGAAAATGGGGAA 57.094 32.000 0.00 0.00 0.00 3.97
2448 2864 7.906199 AATATAACGAATTGGAAAATGGGGA 57.094 32.000 0.00 0.00 0.00 4.81
2449 2865 8.956533 AAAATATAACGAATTGGAAAATGGGG 57.043 30.769 0.00 0.00 0.00 4.96
2582 2998 9.787435 ACCACAACTTAGATAAGACATTGTAAA 57.213 29.630 6.61 0.00 37.08 2.01
2583 2999 9.431887 GACCACAACTTAGATAAGACATTGTAA 57.568 33.333 6.61 0.00 37.08 2.41
2584 3000 8.812972 AGACCACAACTTAGATAAGACATTGTA 58.187 33.333 6.61 0.00 37.08 2.41
2586 3002 9.823647 ATAGACCACAACTTAGATAAGACATTG 57.176 33.333 6.61 3.85 37.08 2.82
2588 3004 8.643324 GGATAGACCACAACTTAGATAAGACAT 58.357 37.037 6.61 0.00 38.79 3.06
2610 3329 8.890718 CGGAGATTATAACAGTTAGATCGGATA 58.109 37.037 0.00 0.00 0.00 2.59
2611 3330 7.628794 GCGGAGATTATAACAGTTAGATCGGAT 60.629 40.741 0.00 0.00 0.00 4.18
2612 3331 6.349115 GCGGAGATTATAACAGTTAGATCGGA 60.349 42.308 0.00 0.00 0.00 4.55
2613 3332 5.800941 GCGGAGATTATAACAGTTAGATCGG 59.199 44.000 0.00 0.00 0.00 4.18
2614 3333 5.800941 GGCGGAGATTATAACAGTTAGATCG 59.199 44.000 0.00 0.00 0.00 3.69
2615 3334 6.100668 GGGCGGAGATTATAACAGTTAGATC 58.899 44.000 0.00 5.48 0.00 2.75
2616 3335 5.542635 TGGGCGGAGATTATAACAGTTAGAT 59.457 40.000 0.00 0.00 0.00 1.98
2617 3336 4.897076 TGGGCGGAGATTATAACAGTTAGA 59.103 41.667 0.00 0.00 0.00 2.10
2618 3337 5.209818 TGGGCGGAGATTATAACAGTTAG 57.790 43.478 0.00 0.00 0.00 2.34
2619 3338 5.617528 TTGGGCGGAGATTATAACAGTTA 57.382 39.130 0.00 0.00 0.00 2.24
2620 3339 4.497291 TTGGGCGGAGATTATAACAGTT 57.503 40.909 0.00 0.00 0.00 3.16
2621 3340 4.497291 TTTGGGCGGAGATTATAACAGT 57.503 40.909 0.00 0.00 0.00 3.55
2622 3341 6.039270 TCAAATTTGGGCGGAGATTATAACAG 59.961 38.462 17.90 0.00 0.00 3.16
2623 3342 5.888724 TCAAATTTGGGCGGAGATTATAACA 59.111 36.000 17.90 0.00 0.00 2.41
2624 3343 6.385649 TCAAATTTGGGCGGAGATTATAAC 57.614 37.500 17.90 0.00 0.00 1.89
2625 3344 6.208599 GGATCAAATTTGGGCGGAGATTATAA 59.791 38.462 17.90 0.00 0.00 0.98
2637 3356 4.276058 ACAAAGCAGGATCAAATTTGGG 57.724 40.909 17.90 4.71 35.64 4.12
2651 3370 1.298264 CGCGCACAAGAACAAAGCA 60.298 52.632 8.75 0.00 0.00 3.91
2689 3408 1.006825 TGAACATCGCGACAACGGAG 61.007 55.000 12.93 0.00 40.15 4.63
2707 3426 6.599437 CCTAACTAAAACAGTCCGACAAATG 58.401 40.000 0.40 0.00 36.04 2.32
2778 3499 0.861837 CTGTTTCTGGACACAGCGAC 59.138 55.000 4.32 0.00 44.54 5.19
2829 3550 2.662535 TGCATAATGGAGGTGATGGG 57.337 50.000 0.00 0.00 0.00 4.00
2849 3571 1.283347 ATGGAGAGAGGCAAAGCAGA 58.717 50.000 0.00 0.00 0.00 4.26
2894 3616 7.606456 ACAAAAATAGTCGGCTCTAATGAAAGA 59.394 33.333 0.00 0.00 0.00 2.52
2898 3620 6.092122 CACACAAAAATAGTCGGCTCTAATGA 59.908 38.462 0.00 0.00 0.00 2.57
2899 3621 6.250819 CACACAAAAATAGTCGGCTCTAATG 58.749 40.000 0.00 0.00 0.00 1.90
2900 3622 5.354234 CCACACAAAAATAGTCGGCTCTAAT 59.646 40.000 0.00 0.00 0.00 1.73
2901 3623 4.693566 CCACACAAAAATAGTCGGCTCTAA 59.306 41.667 0.00 0.00 0.00 2.10
2902 3624 4.250464 CCACACAAAAATAGTCGGCTCTA 58.750 43.478 0.00 0.00 0.00 2.43
2903 3625 3.074412 CCACACAAAAATAGTCGGCTCT 58.926 45.455 0.00 0.00 0.00 4.09
2904 3626 2.414161 GCCACACAAAAATAGTCGGCTC 60.414 50.000 0.00 0.00 35.39 4.70
2905 3627 1.539827 GCCACACAAAAATAGTCGGCT 59.460 47.619 0.00 0.00 35.39 5.52
2906 3628 1.268352 TGCCACACAAAAATAGTCGGC 59.732 47.619 0.00 0.00 38.79 5.54
2907 3629 3.848272 ATGCCACACAAAAATAGTCGG 57.152 42.857 0.00 0.00 0.00 4.79
2908 3630 6.523676 AAAAATGCCACACAAAAATAGTCG 57.476 33.333 0.00 0.00 0.00 4.18
2929 3651 4.891168 GGGTGGAGTTGAAACTAGGAAAAA 59.109 41.667 0.00 0.00 39.88 1.94
2930 3652 4.167307 AGGGTGGAGTTGAAACTAGGAAAA 59.833 41.667 0.00 0.00 39.88 2.29
2931 3653 3.720002 AGGGTGGAGTTGAAACTAGGAAA 59.280 43.478 0.00 0.00 39.88 3.13
2932 3654 3.323775 AGGGTGGAGTTGAAACTAGGAA 58.676 45.455 0.00 0.00 39.88 3.36
2933 3655 2.904434 GAGGGTGGAGTTGAAACTAGGA 59.096 50.000 0.00 0.00 39.88 2.94
2934 3656 2.353803 CGAGGGTGGAGTTGAAACTAGG 60.354 54.545 0.00 0.00 39.88 3.02
2935 3657 2.561419 TCGAGGGTGGAGTTGAAACTAG 59.439 50.000 0.00 0.00 39.88 2.57
2936 3658 2.600790 TCGAGGGTGGAGTTGAAACTA 58.399 47.619 0.00 0.00 39.88 2.24
2937 3659 1.420430 TCGAGGGTGGAGTTGAAACT 58.580 50.000 0.00 0.00 43.16 2.66
2938 3660 2.249844 TTCGAGGGTGGAGTTGAAAC 57.750 50.000 0.00 0.00 0.00 2.78
2939 3661 3.502123 AATTCGAGGGTGGAGTTGAAA 57.498 42.857 0.00 0.00 0.00 2.69


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.